Variant report

Variant	rs3814055
Chromosome Location	chr3:119500035-119500036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10511394	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs10934498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1129708	0.82[ASN][1000 genomes]
rs11926554	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12488820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13089523	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464599	0.94[CHB][hapmap];0.91[CHD][hapmap];0.80[MEX][hapmap]
rs1523127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1523130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608330	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608332	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2461829	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2461830	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472664	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472674	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34255376	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34787921	0.83[ASN][1000 genomes]
rs35576922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4566573	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66840889	0.81[ASN][1000 genomes]
rs7642839	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7643038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289134	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs9817024	0.83[ASN][1000 genomes]
rs9821892	0.83[ASN][1000 genomes]
rs9832958	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865270	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3814055	COX17	cis	lymphoblastoid	seeQTL
rs3814055	HSPBAP1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119497800-119503000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr3:119498200-119501000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:119498800-119500400	Enhancers	Liver	Liver
4	chr3:119498800-119500600	Enhancers	Fetal Intestine Large	intestine
5	chr3:119498800-119500600	Enhancers	Fetal Intestine Small	intestine
6	chr3:119499000-119500400	Weak transcription	Spleen	Spleen
7	chr3:119499200-119501800	Weak transcription	K562	blood
8	chr3:119499200-119502000	Weak transcription	HSMMtube	muscle
9	chr3:119499400-119501200	Weak transcription	HSMM	muscle
10	chr3:119499600-119500200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr3:119499600-119501000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:119499600-119501600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:119499600-119501800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:119499600-119502800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:119499800-119500200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:119500000-119500200	Enhancers	Duodenum Mucosa	Duodenum
17	chr3:119500000-119500200	Enhancers	Small Intestine	intestine
18	chr3:119500000-119500200	Flanking Active TSS	HepG2	liver
19	chr3:119500000-119500400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr3:119500000-119501000	Enhancers	Stomach Mucosa	stomach
21	chr3:119500000-119503200	Active TSS	Rectal Mucosa Donor 29	rectum

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